Contacts of the helix formed by residues 102 - 114 (chain G) in PDB entry 3H2V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 102 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59G ARG* 3.2 22.3 - - - +
100G LEU* 3.3 1.5 - - - +
101G LEU* 1.3 100.4 - - - +
103G GLY* 1.3 63.9 + - - +
104G GLU* 3.1 12.8 + - - +
105G GLN* 3.0 28.2 + - - +
106G ALA 3.1 17.8 + - - -
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Residues in contact with GLY 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G HIS 5.2 8.9 + - - -
58G MET 3.6 19.8 - - - +
59G ARG* 3.9 3.0 - - - +
102G ASN* 1.3 72.9 - - - +
104G GLU* 1.3 68.4 + - - +
106G ALA* 3.5 2.1 + - - +
107G GLU* 3.1 24.6 + - - +
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Residues in contact with GLU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G ASN* 3.1 10.5 + - - +
103G GLY* 1.3 76.9 - - - +
105G GLN* 1.3 65.2 + - + +
107G GLU* 2.9 29.9 + - + +
108G ALA* 3.0 16.5 + - + +
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Residues in contact with GLN 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G ASP 4.2 2.8 + - - -
82G TYR* 3.6 43.6 - - + +
83G GLU* 3.4 18.8 + - - +
100G LEU* 3.6 11.8 - - + +
101G LEU* 3.1 36.8 + - + +
102G ASN* 3.0 27.1 + - - +
104G GLU* 1.3 77.3 - - + +
106G ALA* 1.3 58.4 + - - +
108G ALA* 3.4 1.1 + - - -
109G ALA* 3.0 31.4 + - - +
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Residues in contact with ALA 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G MET 3.7 9.6 - - - +
59G ARG* 3.6 38.4 - - - +
61G ILE* 3.7 15.2 - - + +
100G LEU* 3.9 10.9 - - - +
102G ASN 3.1 7.1 + - - +
103G GLY 3.9 2.2 - - - +
104G GLU 3.3 0.2 - - - -
105G GLN* 1.3 76.2 - - - +
107G GLU* 1.3 57.3 + - - +
109G ALA* 3.9 0.2 - - - +
110G ILE* 2.9 36.2 + - - +
127G LEU* 4.3 5.6 - - + -
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Residues in contact with GLU 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G GLY 3.1 13.4 + - - +
104G GLU* 2.9 27.3 + - - +
106G ALA* 1.3 73.7 - - - +
108G ALA* 1.3 55.5 + - - +
109G ALA 3.1 1.3 - - - -
110G ILE* 3.0 10.2 + - - +
111G ASN* 2.8 55.3 + - - +
127G LEU* 6.0 0.2 - - - -
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Residues in contact with ALA 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G TYR* 3.6 24.2 + - + +
104G GLU 3.0 10.6 + - - +
105G GLN* 4.8 1.1 - - - -
107G GLU* 1.3 76.6 - - - +
109G ALA* 1.3 57.8 + - - +
111G ASN* 3.3 5.8 + - - +
112G ALA* 2.7 37.4 + - - +
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Residues in contact with ALA 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ILE* 4.8 11.7 - - + -
79G LEU* 5.2 2.7 - - + -
82G TYR* 3.7 19.7 + - + -
100G LEU* 3.7 21.1 - - + -
105G GLN 3.0 18.2 + - - +
106G ALA* 3.9 4.3 - - - +
108G ALA* 1.3 78.8 - - - +
110G ILE* 1.3 61.1 + - - +
113G PHE* 3.0 38.2 + - + +
125G VAL* 4.1 2.5 - - - +
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Residues in contact with ILE 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ILE* 3.6 13.2 - - + -
106G ALA 2.9 22.6 + - - +
107G GLU* 3.0 11.0 + - - +
109G ALA* 1.3 76.4 - - - +
111G ASN* 1.3 65.6 + - - +
114G HIS* 2.9 34.0 + - + +
125G VAL* 3.6 29.4 - - + +
126G GLN* 4.1 4.3 - - - -
127G LEU* 3.3 46.9 - - + +
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Residues in contact with ASN 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G GLU* 2.8 41.3 + - - +
108G ALA* 4.0 5.5 - - - +
110G ILE* 1.3 81.6 - - - +
112G ALA* 1.3 63.1 + - - +
113G PHE 3.5 0.2 + - - -
114G HIS* 4.4 5.8 + - - +
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Residues in contact with ALA 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G TYR* 4.2 9.9 - - - +
108G ALA 2.7 21.2 + - - +
109G ALA 4.1 2.5 - - - +
111G ASN* 1.3 74.8 - - - +
113G PHE* 1.3 81.2 + - + +
114G HIS 3.8 1.3 - - - +
116G SER* 4.4 8.5 + - - -
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Residues in contact with PHE 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G LEU* 3.1 50.9 - - + -
79G LEU* 3.6 27.1 - - + -
81G ASP* 6.2 1.6 - - + -
82G TYR* 4.0 21.3 - + - -
109G ALA* 3.0 24.3 + - - +
112G ALA* 1.3 94.9 - - + +
114G HIS* 1.3 61.2 + - - +
115G GLN 3.4 2.1 + - - -
116G SER* 3.2 24.8 + - - +
123G LEU* 3.9 5.8 - - + +
125G VAL* 2.7 28.7 - - + +
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Residues in contact with HIS 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ILE* 2.9 27.2 + - + +
111G ASN* 4.4 5.5 + - - +
112G ALA 3.8 1.4 - - - +
113G PHE* 1.3 71.7 - - - +
115G GLN* 1.3 94.8 + - + +
116G SER* 3.8 0.3 + - - -
124G SER* 3.6 20.3 - - - -
125G VAL* 3.0 40.2 + - - +
126G GLN* 5.7 3.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il